Archive

MRNA-interactionAnnouncing the publication of “Functional transcriptomics in the post-ENCODE era” in Genome Research.

Just a brief post to draw your attention to this article, which was made available in Genome Research as an Advance Online Article on the 30th October.  The article is Open Access… continue reading…  sssssssssaaaasasasasasasasaassasasaaaaaaaaassas

 

numbers_2Less Protein-Coding Genes In GENCODE v18 Than In v17

Shortly after the release of GENCODE v18 last month, our eagle-eyed users noticed that the number of protein-coding genes had fallen by 12 since release v17 (conversation at https://twitter.com/GencodeGenes)…continue reading… asasasasasasasasasasasasasaasasasasasasasasasasasasasasasasasasasasaasasas

info_icon-300x272Attributes: Adding more information to our geneset

We are working on ways to relate more information about the decisions made during the manual annotation process to our users. Currently, in addition to the information captured by biotypes and status, controlled vocabulary attributes are attached to transcripts and/or loci…continue reading… asasasasasasasaaaaaaaasasasasasasasasasasasasasasaasasasasasaasasasasasasasaasasasasass

Screenshot Gencode v15 – a complete first-pass manual annotation of the human genome

GencodeGenes recently attended the Biology of Genomes at the CSHL. Our main message to the conference was an analysis of GENCODE v15. Tim Hubbard detailed the expansion in protein-coding, long non-coding RNA and pseudogene loci across GENCODE releases 3c-15…continue reading…               sasasasasasasasaasaadfsdfdsfsdfsdsdfsdfsd                                                                                                   aaxaxxaxaxaxa

this_way_that_way-300x300Transcriptional complexity: Dual-promoters

As you probably know by now, our remit is not only to capture all human transcripts as models, but also to provide an informed judgment on the functional potential of each model. Often we can do this with a high degree of certainty…continue reading…   aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa   aaaaaaa

TVsOn the annotation of functionality in GENCODE (or: our continuing efforts to understand how a television set works).

Our readers may have seen the ENCODE project discussed once again in the news this past week, and not always in a favourable light. We are, of course, referring to the Genome Biology and Evolution publication…continue reading… aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

What_to_doA single exon locus? What to do, what to do?

When annotating single exon loci, it is hard to get it right. Correct transcriptional start site, correct transcriptional termination site, correct reading frame? It’s hard. Thankfully, we at GENCODE love nothing more than sinking our teeth into a single exon gene…continue reading… aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

Colourful preschool numbersComparing different publicly available genesets against GENCODE 7

We consider GENCODE to be the ideal geneset for analysing transcriptional diversity. In this post, I aim to justify this statement, and compare and contrast both the protein coding and non-coding transcript content of GENCODE with the four other major human genesets that are publicly available…continue reading… aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

Transcriptional_ComplexityThe practical importance of capturing transcriptional complexity in GENCODE

Currently GENCODE contains the largest number of transcripts per loci in any publically available gene build, but why is this important?…continue reading… asasasasssssassaaaaaaaaaaaaaaaaaaaaaaaasssssssasasasasaasasasasasasasasasasasasasasasassaasssssa

GENCODE: Why are there partial transcripts?

If you are just getting acquainted with GENCODE you may be wondering how our genebuild differs from others that are publically available…continue reading…

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Insulin of Mice and Men

Interesting cross-species differences exist between the genes that control blood sugar concentration and here we focus on one involving human and mouse read-through transcripts…continue reading…

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CD99: a tale of functional non-canonical splicing

The canonical ‘GT’ donor and ‘AG’ acceptor splice-sites are only rarely deviated from and, even more rarely, are such events shown to be the driving force behind opposing functions of isoforms from a single locus; however, CD99 provides an interesting example of just that…continue reading… cascasddddddddcsacaaaaaaaaddddaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

The value of comparative annotation: Alternative splicing at the Basigin locus

Recently, we read with interest the Nature publication describing the role of the human basigin protein in facilitating erythrocyte invasion by the malaria parasite. This work, spearheaded at the Wellcome Trust Sanger Institute, indicates that basigin should be considered a target for the development of new anti-malarial therapies…continue reading…aca aaaaaaaaaaaaaaaaaaaacascascsacascsacaaaaaaaaaaaasasasasasasasasaaasasasasaaassaa

Processed Pseudogenes – Junk or Gene?

Processed pseudogenes arise by the integration of cDNA copies of the parent gene at a new locus in the genome. There are 8,426 processed pseudogenes in our Gencode datasets, but are any of these functional?…continue reading…

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